alexhbnr commented 1 year ago

Pull Request

This PR is for a

[x] New Publication(s)
[ ] Correction

For the following list(s):

[x] ancientmetagenome-environmental (README)
[x] ancientmetagenome-hostassociated (README)
[ ] ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): - Klapper 2023 10.1126/science.adf5300

This is to close #1077.

Checklist

[x] Publication is published (preprints currently not accepted)?
[x] Checked the publication is not already in the database?
[x] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
[x] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
[x] Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
[x] Changelog is updated to include the publication under 'Added'?
[ ] Pull request has passed validation checks (see automated comment from github-bot)?
[x] Review requested from @SPAAM-community/ancientmetagenomedir?
[ ] (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here:

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

Invalid dataset ancientmetagenome-environmental_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	archaeological site	feature	553	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error	archaeological site	feature	554	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error	archaeological site	feature	555	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error	archaeological site	feature	556	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error	archaeological site	feature	557	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error	archaeological site	feature	558	'archaeological site' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]

Libraries

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2377	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2378	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2379	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2380	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2381	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2382	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2383	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2384	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2385	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2386	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2387	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2388	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2389	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2390	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2391	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2392	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2393	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2394	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2395	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2396	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2397	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2398	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	PfuTurbo Cx Hotstart DNa	library_polymerase	2399	'PfuTurbo Cx Hotstart DNa' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

SPAAM-community / AncientMetagenomeDir

Klapper2023 #1089

Pull Request

New Publication

Publication Information

Checklist

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental